Description

The oxdna pair styles compute the pairwise-additive parts of the oxDNA force field
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
excluded volume interaction oxdna/excv, the stacking oxdna/stk, cross-stacking oxdna/xstk
and coaxial stacking interaction oxdna/coaxstk as well
as the hydrogen-bonding interaction oxdna/hbond between complementary pairs of nucleotides on
opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
are supported (Sulc).

The exact functional form of the pair styles is rather complex.
The individual potentials consist of products of modulation factors,
which themselves are constructed from a number of more basic potentials
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
We refer to (Ouldridge-DPhil) and (Ouldridge)
for a detailed description of the oxDNA force field.

Note

These pair styles have to be used together with the related oxDNA bond style
oxdna/fene for the connectivity of the phosphate backbone (see also documentation of
bond_style oxdna/fene). Most of the coefficients
in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
Exceptions are the first and second coefficient after oxdna/stk (seq=seqdep and T=0.1 in the above example)
and the first coefficient after oxdna/hbond (seq=seqdep in the above example).
When using a Langevin thermostat, e.g. through fix langevin
or fix nve/dotc/langevin
the temperature coefficients have to be matched to the one used in the fix.

Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
A simple python setup tool which creates single straight or helical DNA strands,
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.

Please cite (Henrich) and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found here.

Restrictions

These pair styles can only be used if LAMMPS was built with the
USER-CGDNA package and the MOLECULE and ASPHERE package. See the Making LAMMPS section for more info on packages.